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<h1 class="title toc-ignore">Installing rsat-core via conda</h1>
<h4 class="author">Jacques van Helden</h4>
<h4 class="date">2020-01-15</h4>
</div>
<hr />
<div id="introduction" class="section level1">
<h1><span class="header-section-number">1</span> Introduction</h1>
<p>This page explains how to install the core package of the Regulatory Sequence Analysis Tools (<strong>rsat-core</strong>) via the <a href="https://docs.conda.io/">conda</a> package manager.</p>
<p>The rsat-core package contains the RSAT command line tools, but no web server or web services.</p>
<hr />
</div>
<div id="requirements" class="section level1">
<h1><span class="header-section-number">2</span> Requirements</h1>
<div id="availability" class="section level2">
<h2><span class="header-section-number">2.1</span> Availability</h2>
<p>The conda package <strong>rsat-core</strong> is available on the <a href="https://anaconda.org/"><strong>anaconda</strong></a> server, in the <a href="https://anaconda.org/bioconda/"><strong>bioconda</strong></a> channel:</p>
<ul>
<li><a href="https://anaconda.org/bioconda/rsat-core" class="uri">https://anaconda.org/bioconda/rsat-core</a></li>
</ul>
</div>
<div id="operating-systems" class="section level2">
<h2><span class="header-section-number">2.2</span> Operating systems</h2>
<ul>
<li><p>The package has been compiled for Linux and Mac OS X.</p></li>
<li><p>It is not directly available as a conda package for Windows, but it could easily be included in a Docker or Singularity container.</p></li>
</ul>
</div>
<div id="miniconda" class="section level2">
<h2><span class="header-section-number">2.3</span> Miniconda</h2>
<p>This tutorial assumes that the conda package manager is installed on your operating system.</p>
<p>If it is not the case, you can easily install <a href="https://docs.conda.io/en/latest/miniconda.html">miniconda3</a>. Note that for this it is not necessary to have admin rights.</p>
<hr />
</div>
</div>
<div id="conda-environment" class="section level1">
<h1><span class="header-section-number">3</span> Conda environment</h1>
<p>It may be convenient to create a specific conda environment rather than in the default environment.</p>
<p><strong>Advantage:</strong> RSAT and all its dependencies are isolated from the other packages installed on your operating system. This may avoid conflicts between incompatible versions of languages or libraries required by other conda packages.</p>
<p><strong>Inconvenient:</strong> the installation may take more space on your storage device since all the dependencies have to be installed in the rsat-specific environment folder.</p>
<p><strong>If you prefer to install rsat-core in the basic conda environment, just skip this section. </strong></p>
<div id="creating-a-conda-environment" class="section level2">
<h2><span class="header-section-number">3.1</span> Creating a conda environment</h2>
<div class="sourceCode" id="cb1"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="ex">conda</span> create -n rsat</a></code></pre></div>
<p>Check that the environment has well been created</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="ex">conda</span> env list</a>
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="ex">conda</span> env list <span class="kw">|</span> <span class="fu">grep</span> rsat</a></code></pre></div>
</div>
<div id="activating-the-rsat-environment" class="section level2">
<h2><span class="header-section-number">3.2</span> Activating the rsat environment</h2>
<p>We will now activate the newly created conda environemnt <code>rsat</code> and check its package content.</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="ex">conda</span> activate rsat</a></code></pre></div>
<p>The name of the current conda environment should appear at the beginning of your prompt, for example:</p>
<p><code>(rsat) %</code></p>
<p>In principle, at this stage, the environment should contain no package since we just created it. We can check this by listing the packages.</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="ex">conda</span> list <span class="co">## List the packages in the environment</span></a></code></pre></div>
<hr />
</div>
</div>
<div id="installing-rsat-core" class="section level1">
<h1><span class="header-section-number">4</span> Installing rsat-core</h1>
<div class="sourceCode" id="cb5"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="ex">conda</span> install -c bioconda rsat-core</a></code></pre></div>
<hr />
<div id="temporary-patches" class="section level2">
<h2><span class="header-section-number">4.1</span> Temporary patches</h2>
<p>In the 2020.01.04 release, some Perl libraries are still missing from conda.</p>
<p>We will soon package them for conda. In the meantime, it is easy to install them manually using <code>cpan</code> (especially if you created a conda environment for rsat, in which case you don’t need admin rights to install Perl modules in the environment).</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="co">## Activate the conda environment </span></a>
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="co">## </span></a>
<a class="sourceLine" id="cb6-3" data-line-number="3"><span class="co">## Choose either base or rsat depending on your configuration</span></a>
<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="ex">conda</span> activate</a>
<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="ex">conda</span> activate rsat</a>
<a class="sourceLine" id="cb6-6" data-line-number="6"></a>
<a class="sourceLine" id="cb6-7" data-line-number="7"><span class="ex">cpan</span> install Statistics::Distributions</a>
<a class="sourceLine" id="cb6-8" data-line-number="8"><span class="ex">cpan</span> install Email::Sender::Simple</a>
<a class="sourceLine" id="cb6-9" data-line-number="9"><span class="ex">cpan</span> install Parallel::ForkManager</a>
<a class="sourceLine" id="cb6-10" data-line-number="10"><span class="ex">cpan</span> install MCE::Shared</a></code></pre></div>
<hr />
</div>
</div>
<div id="testing-the-rsat-core-environment" class="section level1">
<h1><span class="header-section-number">5</span> Testing the rsat-core environment</h1>
<p>We can perform a quick test of the rsat-core package.</p>
<div id="locating-the-rsat-command" class="section level2">
<h2><span class="header-section-number">5.1</span> Locating the rsat command</h2>
<p>We will first locate the <code>rsat</code> command.</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="fu">which</span> rsat</a></code></pre></div>
</div>
<div id="listing-rsat-subcommands" class="section level2">
<h2><span class="header-section-number">5.2</span> Listing rsat subcommands</h2>
<p>The <code>rsat</code> command enables to run all the RSAT tools as sub-commands. We can list them with the option <code>--list</code>, or get a short description with the option <code>--help</code>.</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="ex">rsat</span> --list <span class="co">## List the names of RSAT subcommands</span></a>
<a class="sourceLine" id="cb8-2" data-line-number="2"><span class="ex">rsat</span> --list <span class="kw">|</span> <span class="fu">wc</span> -l <span class="co">## count the number of supported RSAT subcommands</span></a>
<a class="sourceLine" id="cb8-3" data-line-number="3"><span class="ex">rsat</span> --help <span class="co">## Get a short description of the RSAT subcommands</span></a></code></pre></div>
</div>
<div id="getting-help-for-an-rsat-subcommand" class="section level2">
<h2><span class="header-section-number">5.3</span> Getting help for an rsat subcommand</h2>
<p>The help page of an RSAT command can be obtained by running</p>
<p><code>rsat [subcommand] -h</code></p>
<p>For example:</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb9-1" data-line-number="1"><span class="ex">rsat</span> random-seq -h</a></code></pre></div>
</div>
<div id="testing-some-rsat-commands" class="section level2">
<h2><span class="header-section-number">5.4</span> Testing some RSAT commands</h2>
<p>Generate 3 random sequences of length 100.</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="ex">rsat</span> random-seq -l 100 -n 3</a></code></pre></div>
<p>Generate random sequences and send them as input to <code>oligo-analysis</code> to count the dinucleotide occurrences. Note that the result of an RSAT command can be directly used as input by another command with the pipe symbol <code>|</code>.</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb11-1" data-line-number="1"><span class="ex">rsat</span> random-seq -l 100 -n 3 \</a>
<a class="sourceLine" id="cb11-2" data-line-number="2"> <span class="kw">|</span> <span class="ex">rsat</span> oligo-analysis -v 1 -l 2 -1str -return occ,freq</a></code></pre></div>
</div>
<div id="locating-the-rsat-components" class="section level2">
<h2><span class="header-section-number">5.5</span> Locating the RSAT components</h2>
<p>The path of the RSAT components depends on your local configuration of conda.</p>
<p>You can find them as subfolders of the conda path, which may itself be generic (base environment) or specific to rsat (rsat environment).</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="bu">echo</span> <span class="va">$CONDA_PREFIX</span></a></code></pre></div>
<p>The rsat command is found in the bin directory, together with some RSAT compiled programs (e.g. <code>count-words</code>, <code>matrix-scan-quick</code>, <code>variation-scan</code>). All the programs found in this bin directory are automatically in your path as soon as you activate conda.</p>
<p>The two following commands should in principle return the same path.</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb13-1" data-line-number="1"><span class="bu">echo</span> <span class="va">$CONDA_PREFIX</span>/bin/rsat</a>
<a class="sourceLine" id="cb13-2" data-line-number="2"><span class="fu">which</span> rsat</a></code></pre></div>
<p>Additional files of the RSAT suite are found in the folder <code>share/rsat</code> of the conda directory.</p>
<div class="sourceCode" id="cb14"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb14-1" data-line-number="1"><span class="fu">ls</span> -l <span class="va">$CONDA_PREFIX</span>/share/rsat</a></code></pre></div>
<p>This includes Perl, python, R scripts, makefiles, as well as RSAT configuration files.</p>
</div>
<div id="a-battery-of-tests-for-rsat-subcommands" class="section level2">
<h2><span class="header-section-number">5.6</span> A battery of tests for rsat subcommands</h2>
<p>RSAT includes a set of tests for different commands, which can be run individually via a makefile.</p>
<div class="sourceCode" id="cb15"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="bu">export</span> <span class="va">RSAT=$CONDA_PREFIX</span>/share/rsat</a>
<a class="sourceLine" id="cb15-2" data-line-number="2"><span class="fu">make</span> -f <span class="va">$RSAT</span>/makefiles/subcommand_tests.mk</a></code></pre></div>
<p>This displays the list of <code>make</code> targets, which can be called individually by appending them to the previous command. For example, we can run the target <code>randseq</code> in order to test the RSAT program <code>random-seq</code>.</p>
<div class="sourceCode" id="cb16"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb16-1" data-line-number="1"><span class="fu">make</span> -f <span class="va">$RSAT</span>/makefiles/subcommand_tests.mk randseq</a></code></pre></div>
<p>This will generate a random sequence, store it in a local file, and display the path on the result. The same can be done for each other target. The full RSAT command is systematically displayed, which indicates the parameters used for some typical analyses.</p>
<p>The target <code>all</code> runs all the test commands (this can take some time, because it includes downloading the yeast genome, running the <code>peak-motifs</code> workflow, …).</p>
</div>
<div id="optional-direct-access-to-each-tool" class="section level2">
<h2><span class="header-section-number">5.7</span> Optional: direct access to each tool</h2>
<div class="sourceCode" id="cb17"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb17-1" data-line-number="1"><span class="co">## Before: the individual RSAT Perl and python scripts are not in the path</span></a>
<a class="sourceLine" id="cb17-2" data-line-number="2"><span class="fu">which</span> random-seq ## a Perl script</a>
<a class="sourceLine" id="cb17-3" data-line-number="3"><span class="fu">which</span> random-motif ## a python script</a>
<a class="sourceLine" id="cb17-4" data-line-number="4"></a>
<a class="sourceLine" id="cb17-5" data-line-number="5"><span class="co">## Load the bashrc file with RSAT environment variables</span></a>
<a class="sourceLine" id="cb17-6" data-line-number="6"><span class="bu">cd</span> <span class="va">$CONDA_PREFIX</span>/share/rsat</a>
<a class="sourceLine" id="cb17-7" data-line-number="7"><span class="bu">source</span> RSAT_config.bashrc</a>
<a class="sourceLine" id="cb17-8" data-line-number="8"></a>
<a class="sourceLine" id="cb17-9" data-line-number="9"><span class="co">## After: the Perl and python scripts are now in the path</span></a>
<a class="sourceLine" id="cb17-10" data-line-number="10"><span class="fu">which</span> random-seq ## a Perl script</a>
<a class="sourceLine" id="cb17-11" data-line-number="11"><span class="fu">which</span> random-motif ## a python script</a></code></pre></div>
<p>After having loaded <code>RSAT_config.bashrc</code>, the commands are avaiable in the path, and can thus be invoked directly (e.g. running <code>random-seq -l 100</code> would do the same as <code>rsat random-seq -l 100</code>).</p>
<hr />
</div>
</div>
<div id="uninstalling-rsat-core" class="section level1">
<h1><span class="header-section-number">6</span> Uninstalling rsat-core</h1>
<p>To uninstall rsat-core, you should simply remove the package from conda. The way to proceed depends on whether you installed rsat-core in a specific conda environment (rsat) or in the base environment.</p>
<div id="uninstalling-rsat-core-from-the-base-environment" class="section level2">
<h2><span class="header-section-number">6.1</span> Uninstalling rsat-core from the base environment</h2>
<div class="sourceCode" id="cb18"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb18-1" data-line-number="1"><span class="ex">conda</span> activate ## Activate the base environment</a>
<a class="sourceLine" id="cb18-2" data-line-number="2"><span class="ex">conda</span> remove rsat-core</a></code></pre></div>
</div>
<div id="uninstalling-the-rsat-conda-environment-and-all-its-packages" class="section level2">
<h2><span class="header-section-number">6.2</span> Uninstalling the rsat conda environment (and all its packages)</h2>
<div class="sourceCode" id="cb19"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb19-1" data-line-number="1"><span class="ex">conda</span> deactivate <span class="co">## make sure you are not in the rsat environment</span></a>
<a class="sourceLine" id="cb19-2" data-line-number="2"><span class="ex">conda</span> remove -n rsat --all</a></code></pre></div>
<hr />
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